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I found out the problem myself. In Illustrator: when opening a layer, it is possible to see all the paths in the drawing in a big list. If you search this list for groups, you will find "clipped paths" inside them. If you delete those, it is possible to use the Live Paint Bucket tool.

Also: apparently Revit has some difficulty in converting the 3D model to pdf, since there where some gaps here and there (and the "clipped paths problem of course"), so I had to make a few extra paths in order to complete certain areas.

But in the end, it al worked with a bit of effort